6G52 | pdb_00006g52

CRYSTAL STRUCTURE OF THE CNMP BINDING DOMAIN OF THE MAGNESIUM TRANSPORTER CNNM4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 
    0.303 (Depositor), 0.306 (DCC) 
  • R-Value Work: 
    0.284 (Depositor), 0.285 (DCC) 
  • R-Value Observed: 
    0.286 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6G52

This is version 1.3 of the entry. See complete history

Literature

Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4.

Gimenez-Mascarell, P.Oyenarte, I.Gonzalez-Recio, I.Fernandez-Rodriguez, C.Corral-Rodriguez, M.A.Campos-Zarraga, I.Simon, J.Kostantin, E.Hardy, S.Diaz Quintana, A.Zubillaga Lizeaga, M.Merino, N.Diercks, T.Blanco, F.J.Diaz Moreno, I.Martinez-Chantar, M.L.Tremblay, M.L.Muller, D.Siliqi, D.Martinez-Cruz, L.A.

(2019) Int J Mol Sci 20

  • DOI: https://doi.org/10.3390/ijms20246279
  • Primary Citation Related Structures: 
    6G52, 6RS2

  • PubMed Abstract: 

    The four member family of "Cyclin and Cystathionine β-synthase (CBS) domain divalent metal cation transport mediators", CNNMs, are the least-studied mammalian magnesium transport mediators. CNNM4 is abundant in the brain and the intestinal tract, and its abnormal activity causes Jalili Syndrome. Recent findings show that suppression of CNNM4 in mice promotes malignant progression of intestinal polyps and is linked to infertility. The association of CNNM4 with phosphatases of the regenerating liver, PRLs, abrogates its Mg 2+ -efflux capacity, thus resulting in an increased intracellular Mg 2+ concentration that favors tumor growth. Here we present the crystal structures of the two independent intracellular domains of human CNNM4, i.e., the Bateman module and the cyclic nucleotide binding-like domain (cNMP). We also derive a model structure for the full intracellular region in the absence and presence of MgATP and the oncogenic interacting partner, PRL-1. We find that only the Bateman module interacts with ATP and Mg 2+ , at non-overlapping sites facilitating their positive cooperativity. Furthermore, both domains dimerize autonomously, where the cNMP domain dimer forms a rigid cleft to restrict the Mg 2+ induced sliding of the inserting CBS1 motives of the Bateman module, from a twisted to a flat disk shaped dimer.


  • Organizational Affiliation
    • Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain.

Macromolecule Content 

  • Total Structure Weight: 192.67 kDa 
  • Atom Count: 9,252 
  • Modeled Residue Count: 1,249 
  • Deposited Residue Count: 1,701 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metal transporter CNNM4189Homo sapiensMutation(s): 0 
Gene Names: CNNM4ACDP4KIAA1592
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P4Q7 (Homo sapiens)
Explore Q6P4Q7 
Go to UniProtKB:  Q6P4Q7
PHAROS:  Q6P4Q7
GTEx:  ENSG00000158158 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P4Q7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth I]
B
C
D
E
A [auth I],
B,
C,
D,
E,
F,
G,
H,
I [auth A]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free:  0.303 (Depositor), 0.306 (DCC) 
  • R-Value Work:  0.284 (Depositor), 0.285 (DCC) 
  • R-Value Observed: 0.286 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.738α = 90
b = 116.738β = 90
c = 243.459γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2013-47531-R
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-77408-R
Spanish Ministry of Economy and CompetitivenessSpainCSD2008-00005
Spanish Ministry of Economy and CompetitivenessSpainSEV-2016-0644
Spanish Ministry of Economy and CompetitivenessSpainBES-2014-068464

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Structure summary